One of my ponds has suffered a bit of a disaster this year. Despite it being the mildest winter for some while, the old plastic shell of the pond sprung a leak. I went out one bright (early) spring morning to find it almost empty, except for a tangle of drying weed and muddy sludge in the bottom.
The solution will be to lift the surrounding edging stones, line the shell with a flexible rubber liner, and replace the stones again - and in fact a dear gardening friend acted nobly to help me get to work on sorting out the mess, insistently lifting most of the stones for me despite my exhortations to *not* go out in the pouring rain to do navvy type work (she had been away from her garden for a few days and was suffering withdrawal symptoms!).
Even this kindness came back to bite, however, as a few weeks later, we had a day of torrential rain onto already soaked land; having a naturally high water table here anyway, the unexpected - but in hindsight inevitable - result occurred. With nothing to hold it down, the shell rose up like Noah's Ark above the Deluge! 
A day later it had subsided again, but has continued to sit, sulking, in the corner of the garden, waiting for action to be taken; I have been removing some of the sludge (decomposing leaves, mostly) bit by bit. My concern after the initial leak was for the welfare of the newts which I knew lived in the pond, so I had already removed the pondweed in which I thought (hoped) they would be lurking, and indeed did recover a couple of creatures over the weeks that followed.
The baking heat over this last weekend saw even more progress on the moving of the debris, drying it out and making removal easier. The remaining water was down to just a centimetre or so, so imagine my surprise - and concern - when scraping mud from the bottom to find three more newts, barely moving and just clinging on to life, it seemed, with a great deal of effort. But imagine also my pleasure at being able to move them all, from the Mud Puddle of Misery down to the cool and relatively clear waters of the bottom pond, where I hope life will be more tolerable for them. From their barely mobile activity when I dredged them from the mud, it was a happy sight to see them swim off into the depths of their new home with quickly restored vigour. 
The dragonfly nymphs and other mud-living creatures are important as well, of course - but pond bottom debris is their more natural habitat, so they can stay where they are; I'm not so concerned about them. I am making sure that the mud remains mud for them to complete their life cycles and there are leaf piles and wood boards into the pond to allow other creatures to climb out. (I also check daily). But for now, at least, the newts and I are feeling much happier about life…while the mud removal and pond repair continues as 'work in progress'!
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